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Source code for galaxy.jobs.output_checker

import re
import traceback
from logging import getLogger

from galaxy.tools.parser.error_level import StdioErrorLevel
from galaxy.util import unicodify
from galaxy.util.bunch import Bunch

log = getLogger(__name__)



[docs]def check_output(tool, stdout, stderr, tool_exit_code, job): """ Check the output of a tool - given the stdout, stderr, and the tool's exit code, return DETECTED_JOB_STATE.OK if the tool exited succesfully or error type otherwise. No exceptions should be thrown. If this code encounters an exception, it returns OK so that the workflow can continue; otherwise, a bug in this code could halt workflow progress. Note that, if the tool did not define any exit code handling or any stdio/stderr handling, then it reverts back to previous behavior: if stderr contains anything, then False is returned. """ # By default, the tool succeeded. This covers the case where the code # has a bug but the tool was ok, and it lets a workflow continue. state = DETECTED_JOB_STATE.OK stdout = unicodify(stdout) stderr = unicodify(stderr) try: # Check exit codes and match regular expressions against stdout and # stderr if this tool was configured to do so. # If there is a regular expression for scanning stdout/stderr, # then we assume that the tool writer overwrote the default # behavior of just setting an error if there is *anything* on # stderr. if len(tool.stdio_regexes) > 0 or len(tool.stdio_exit_codes) > 0: # Check the exit code ranges in the order in which # they were specified. Each exit_code is a StdioExitCode # that includes an applicable range. If the exit code was in # that range, then apply the error level and add a message. # If we've reached a fatal error rule, then stop. max_error_level = StdioErrorLevel.NO_ERROR if tool_exit_code is not None: for stdio_exit_code in tool.stdio_exit_codes: if (tool_exit_code >= stdio_exit_code.range_start and tool_exit_code <= stdio_exit_code.range_end): # Tack on a generic description of the code # plus a specific code description. For example, # this might prepend "Job 42: Warning (Out of Memory)\n". code_desc = stdio_exit_code.desc if None is code_desc: code_desc = "" tool_msg = ("%s: Exit code %d (%s)" % ( StdioErrorLevel.desc(stdio_exit_code.error_level), tool_exit_code, code_desc)) log.info("Job %s: %s" % (job.get_id_tag(), tool_msg)) stderr = tool_msg + "\n" + stderr max_error_level = max(max_error_level, stdio_exit_code.error_level) if max_error_level >= StdioErrorLevel.MAX: break if max_error_level < StdioErrorLevel.FATAL: # We'll examine every regex. Each regex specifies whether # it is to be run on stdout, stderr, or both. (It is # possible for neither stdout nor stderr to be scanned, # but those regexes won't be used.) We record the highest # error level, which are currently "warning" and "fatal". # If fatal, then we set the job's state to ERROR. # If warning, then we still set the job's state to OK # but include a message. We'll do this if we haven't seen # a fatal error yet for regex in tool.stdio_regexes: # If ( this regex should be matched against stdout ) # - Run the regex's match pattern against stdout # - If it matched, then determine the error level. # o If it was fatal, then we're done - break. # Repeat the stdout stuff for stderr. # TODO: Collapse this into a single function. if regex.stdout_match: regex_match = re.search(regex.match, stdout, re.IGNORECASE) if regex_match: rexmsg = __regex_err_msg(regex_match, regex) log.info("Job %s: %s" % (job.get_id_tag(), rexmsg)) stdout = rexmsg + "\n" + stdout max_error_level = max(max_error_level, regex.error_level) if max_error_level >= StdioErrorLevel.FATAL: break if regex.stderr_match: regex_match = re.search(regex.match, stderr, re.IGNORECASE) if regex_match: rexmsg = __regex_err_msg(regex_match, regex) log.info("Job %s: %s" % (job.get_id_tag(), rexmsg)) stderr = rexmsg + "\n" + stderr max_error_level = max(max_error_level, regex.error_level) if max_error_level >= StdioErrorLevel.FATAL: break # If we encountered a fatal error, then we'll need to set the # job state accordingly. Otherwise the job is ok: if max_error_level == StdioErrorLevel.FATAL_OOM: state = DETECTED_JOB_STATE.OUT_OF_MEMORY_ERROR elif max_error_level >= StdioErrorLevel.FATAL: log.debug("Tool exit code indicates an error, failing job.") state = DETECTED_JOB_STATE.GENERIC_ERROR else: state = DETECTED_JOB_STATE.OK # When there are no regular expressions and no exit codes to check, # default to the previous behavior: when there's anything on stderr # the job has an error, and the job is ok otherwise. else: # TODO: Add in the tool and job id: # log.debug( "Tool did not define exit code or stdio handling; " # + "checking stderr for success" ) if stderr: state = DETECTED_JOB_STATE.GENERIC_ERROR else: state = DETECTED_JOB_STATE.OK if DETECTED_JOB_STATE != DETECTED_JOB_STATE.OK and stderr: if stderr: peak = stderr[0:ERROR_PEAK] log.debug("job failed, standard error is - [%s]" % peak) # On any exception, return True. except Exception: tb = traceback.format_exc() log.warning("Tool check encountered unexpected exception; " + "assuming tool was successful: " + tb) state = DETECTED_JOB_STATE.OK # Store the modified stdout and stderr in the job: if job is not None: job.set_streams(stdout, stderr) return state
def __regex_err_msg(match, regex): """ Return a message about the match on tool output using the given ToolStdioRegex regex object. The regex_match is a MatchObject that will contain the string matched on. """ # Get the description for the error level: err_msg = StdioErrorLevel.desc(regex.error_level) + ": " # If there's a description for the regular expression, then use it. # Otherwise, we'll take the first 256 characters of the match. if None is not regex.desc: err_msg += regex.desc else: mstart = match.start() mend = match.end() err_msg += "Matched on " # TODO: Move the constant 256 somewhere else besides here. if mend - mstart > 256: err_msg += match.string[mstart : mstart + 256] + "..." else: err_msg += match.string[mstart: mend] return err_msg